template.CMS.C: Mouse CMS template (option C)

In MolecularPathologyLab/MmCMS: Calling CMS for mouse tissue

Mouse CMS template (option C)

Description

Mouse CMS template (option C)

Usage

template.CMS.C

Format

An object of class data.frame with 77 rows and 2 columns.

Details

CMS prediction template for NTP method. Marker genes were identified through a more complicated approach. A combined pathway system encompassing multiple biological and histological signalling cascades. templates$probe refers to gene sets.

References

Eide PW, Bruun J, Lothe RA, Sveen A. CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models. Scientific reports (2017)

Guinney J, Dienstmann R, Wang X, de Reynies A, et al. The consensus molecular subtypes of colorectal cancer. Nat Med (2015)

Hoshida Y. Nearest Template Prediction: A Single-Sample-Based Flexible Class Prediction with Confidence Assessment. PLoS ONE. (2010)

Liberzon et al. The Molecular Signatures Database Hallmark Gene Set Collection. Cell Syst (2015)

Petitprez, F., Lévy, S., Sun, C.-M., Meylan, M., et al. The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression. Genome Med (2020)

Hänzelmann S., Castelo R. and Guinney J. GSVA: gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 14:7, 2013.

Examples

emat <- TestData_gemm
re <- MmCMS(emat, templates=MmCMS::template.CMS.C, Genesets = c("template.CMS.C"), seed=120)

MolecularPathologyLab/MmCMS documentation built on Oct. 18, 2023, 10:42 p.m.